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- PDB-8vfw: Crystal Structure of V113N D-Dopachrome Tautomerase (D-DT) -

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Basic information

Entry
Database: PDB / ID: 8vfw
TitleCrystal Structure of V113N D-Dopachrome Tautomerase (D-DT)
ComponentsD-dopachrome decarboxylase
KeywordsISOMERASE / Truncation / Enzyme / Cytokine
Function / homology
Function and homology information


D-dopachrome decarboxylase / D-dopachrome decarboxylase activity / dopachrome isomerase activity / melanin biosynthetic process / phenylpyruvate tautomerase activity / cytokine receptor binding / negative regulation of macrophage chemotaxis / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / positive regulation of ERK1 and ERK2 cascade ...D-dopachrome decarboxylase / D-dopachrome decarboxylase activity / dopachrome isomerase activity / melanin biosynthetic process / phenylpyruvate tautomerase activity / cytokine receptor binding / negative regulation of macrophage chemotaxis / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / positive regulation of ERK1 and ERK2 cascade / extracellular space / extracellular exosome / cytoplasm
Similarity search - Function
Macrophage migration inhibitory factor, conserved site / Macrophage migration inhibitory factor family signature. / Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily
Similarity search - Domain/homology
CITRIC ACID / D-dopachrome decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsParkins, A. / Wolff, A. / Thompson, M.C. / Pantouris, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: The C-terminal Region of D-DT Regulates Molecular Recognition for Protein-Ligand Complexes.
Authors: Parkins, A. / Pilien, A.V.R. / Wolff, A.M. / Argueta, C. / Vargas, J. / Sadeghi, S. / Franz, A.H. / Thompson, M.C. / Pantouris, G.
History
DepositionDec 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-dopachrome decarboxylase
B: D-dopachrome decarboxylase
C: D-dopachrome decarboxylase
D: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6265
Polymers50,4344
Non-polymers1921
Water9,980554
1
A: D-dopachrome decarboxylase

A: D-dopachrome decarboxylase

A: D-dopachrome decarboxylase


Theoretical massNumber of molelcules
Total (without water)37,8253
Polymers37,8253
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area5730 Å2
ΔGint-28 kcal/mol
Surface area13720 Å2
MethodPISA
2
B: D-dopachrome decarboxylase
C: D-dopachrome decarboxylase
D: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0184
Polymers37,8253
Non-polymers1921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-24 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.239, 111.239, 65.973
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-332-

HOH

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Components

#1: Protein
D-dopachrome decarboxylase / D-dopachrome tautomerase / Phenylpyruvate tautomerase II


Mass: 12608.498 Da / Num. of mol.: 4 / Mutation: V113N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDT / Production host: Escherichia coli (E. coli) / References: UniProt: P30046, D-dopachrome decarboxylase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 26-32% PEG 4000, 0.1M Sodium Citrate (pH 5.2-6.8), 0.2M Ammonium Acetate
PH range: 5.2-5.8

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.31→96.34 Å / Num. obs: 111333 / % possible obs: 99.9 % / Redundancy: 17.1 % / CC1/2: 1 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.017 / Rrim(I) all: 0.075 / Net I/σ(I): 12.4 / Num. measured all: 1906424
Reflection shellResolution: 1.31→1.33 Å / % possible obs: 98.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.881 / Num. measured all: 42192 / Num. unique obs: 5498 / CC1/2: 0.767 / Rpim(I) all: 0.338 / Rrim(I) all: 0.945 / Net I/σ(I) obs: 0.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→96.34 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22153 5701 5.1 %RANDOM
Rwork0.18973 ---
obs0.1913 105609 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.37 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.31→96.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 13 561 3814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133316
X-RAY DIFFRACTIONr_bond_other_d0.0350.0153205
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.6344500
X-RAY DIFFRACTIONr_angle_other_deg2.4411.5687366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7975430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0621.342149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14715527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8231523
X-RAY DIFFRACTIONr_chiral_restr0.0780.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023742
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02740
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7652.1461735
X-RAY DIFFRACTIONr_mcbond_other1.7582.1451734
X-RAY DIFFRACTIONr_mcangle_it2.4953.212160
X-RAY DIFFRACTIONr_mcangle_other2.4943.212161
X-RAY DIFFRACTIONr_scbond_it2.7892.3951581
X-RAY DIFFRACTIONr_scbond_other2.7882.3961582
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1663.4862341
X-RAY DIFFRACTIONr_long_range_B_refined5.83328.5933787
X-RAY DIFFRACTIONr_long_range_B_other5.52227.4743620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.31→1.344 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 494 -
Rwork0.384 7622 -
obs--98.65 %

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